Microbial Ecology PDF

Microbial Ecology  Microbial ecology: systematic study of inter-relationships which exist between living organisms & components of environment: 1. Biotic (living) components; as plants, animals, & bacteria 2. Abiotic (non-living) comp...

Microbial Ecology  Microbial ecology: systematic study of inter-relationships which exist between living organisms & components of environment: 1. Biotic (living) components; as plants, animals, & bacteria 2. Abiotic (non-living) components; as water, soil, & atmosphere Symbiosis (symbiotic relationship)  Two dissimilar (different spp.) symbionts living together or in close association.  4 types: 1. Neutralism  neither symbiont is affected by relationship (at the same ecologic niche) 2. Commensalism  beneficial to only one symbiont & neither beneficial nor harmful to other  neither organism is physiologically dependent on the other  Examples:  Many MOs of indigenous microflora of humans  Blackhead Mite (Demodex) Demodicosis (not a disease) - Tiny elongated body, lives in human facial; mites demodex  small hair follicles D. folliculorum arachnid  pilosebaceous glands D. brevis arthropods ticks insicts - eyelashes - Prevention: face cleansing, periodic exfoliating, & avoid oil-based makeup - Rx: permethrin cream or Sulphur ointment.  Furuncular myiasis - Caused by Dermatobia hominis (human bot fly) - symbiont is mechanically transported by its host - endemic in Central & South America - Female lay & attach eggs on other zoophilic blood-feeding porter vectors (mostly flies, or mosquitoes or ticks). - When porter vectors bite host, eggs hatch & released larvae introduced into skin of human host through bite wound→ Boil-like lesions. - Maggots: fly larvae 3. Mutualism  beneficial to both symbionts (mutually beneficial)  Humans: Many MOs of indigenous intestinal normal microflora (space & nutrients)  E. coli (vitamin K production).  Examples:  Medicinal Leeches - FDA approval - Used for people with history of: abscesses, wounds & Recently venous congestion after plastic surgery 1  - Aeromonas spp  GNB, normal flora in gut of leeches  Aeromonas  essential for digestion of blood (nutrients to both) as leeches cant digest blood - Leeches cause wound Infection due to Aeromonas (primarily A. veronii)  concomitant prophylactic antibiotic must be prescribed  Termites (small insects) - eat wood but can’t digest it - intestinal protozoa;  warm moist space & nutrients  break down large wood molecules into smaller cellulose molecules - cellulose: easily absorbed & food for both organisms  Lichen - grown on tree trunks & rocks - Composed of fungi + algae:  Fungus: hyphal cell wall’s chitin alga protection from desiccation  Alga photosynthesis (CHOs & energy for both). 4. Parasitism  beneficial to one symbiont (parasite) & detrimental (tend to be harmful) to the other symbiont (host):  Nonpathogenic: only dumb parasites kill their hosts  Pathogenic (disease causing/ fatal) → African sleeping sickness  Change of symbiotic relationships o conditions which can change commensalistic or mutualistic between humans & their indigenous microflora (many are opportunists) into parasitic - Healthy IS↑: change of anatomical site habitat - IS↓ - Burns, lacerations, wounds, & surgery Human Indigenous Microbiota (Normal Flora) 1. Resident  Include all microbes (bacteria, fungi, protozoa, & viruses) which reside on or within body.  Their number is ≈ 10 times × total number of our different body cells = 1014 (500-1000 different bacterial species).  humans are only 10% “human” & 90% bacterial.  Body fluids (Blood, Lymph & CSF), & most internal tissues & organs: sterile (Free of MOs).  Destruction of microflora→ SUPERINFECTION 2  2. Transient  Microflora from external environment taking residence on or within body only TEMPORARY; - washed by bathing - killed by toxins of resident flora - flushed away by body excretions & secretions (urine, tears, & sweat) - fails to survive in acidic or alkaline pH  Beneficial Role 1. Production of Vitamins:  by intestinal flora  as vitamin K, folic acid, B12 (cyanocobalamin), B1 (Thiamine), B2, B7 (biotin), B6 (pyridoxine), B5 (pantothenic acid). 2. Constant source of antigens stimulating immune system. 3. Microbial Antagonism:  Prevention of opportunistic pathogens’ overgrowth & colonization  by competing for nutrients & colonization sites (Colonization Resistance) & production of bacteriocins Bactriocins antibiotics Antibacterial proteins produced by certain Antibacterial chemical substances produced bacterial strains. by soil- living MO, molds & bacteria. Ex: colicin of Ecoli More potent Less potent Narrower spectrum Wider activity spectrum Used for epidemiological bacterial typing Used as a treatment of bacterial infections.  Some of the microbes that inhabit our bodies are known as opportunistic pathogens (or opportunist). Although these microbes usually don’t cause any problems to us, but it could do so in cases of: 1. Change of anatomical site habitat: harmless intestinal E coli → serious infections in Urinary bladder, Blood Stream, lungs, wounds, & others. 2. Prolonged use of broad-spectrum antibiotics → reduction of indigenous microflora → SUPERINFECTION (overgrowth of opportunistic MOs which are usually present only in small numbers):  C difficile (in colon) → antibiotic associated diarrhea(AAD) & pseudomembranous colitis (PMC).  C albicans (yeast)→ candidiasis (moniliasis) → (in mouth: thrush or in vagina: yeast vaginitis). 3. Increase vaginal pH: C albicans → vaginitis. 4. IS↓ due to disease & chemoreactions. 5. Other conditions as burns, lacerations, wounds, & surgical procedures. 3 Microflora of different anatomical sites  Skin o Most of skin resident microflora are anaerobes in (deeper skin layers, hair follicles, sweat, & sebaceous glands) o Most common bacteria:  Staph: S.epidermidis & CONS  Corynebacterium/ Diphtheroids  pathogenic and cause diphtheria  Propionibacterium (Acne) o Most common fungus: C albicans o Hand washing→  infections o Burns, lacerations, wounds, & surgery→ skin Infection  Ears & Eyes o Outer ear & auditory canal: same as flora on skin o Middle & inner ear: sterile o Conjunctiva; despite tears’ mechanical flow, lysozyme E, & antimicrobial substances  Staph, Strep, Diphtheroids & Moraxella catarrhalis  Respiratory tract o Lower RT (larynx  alveoli): usually sterile o Upper RT = nose & throat (pharynx) with moist warm mucus membranes - Harmless: Diphtheroids, Lactobacilli & Micrococci - Opportunistic: Strep, Staph, Neisseria & Corynebacterium.  Oral Cavity (Mouth) o Anaerobic (gum margins, crevices between teeth, & tonsils’ deep folds) & aerobic bacteria. o  Dental hygiene→ Dental caries, gingivitis & more severe periodontal diseases o Bacteria, yeasts, protozoa & viruses o Bacteria includes:  GPC: Staph, Strep  GPB: Corynebacterium, Lactobacillus, Actinomyces, Propionibacterium  GNC: Neisseria, Veillonella  GNB: Hemophilus, Fusobacterium, Porphyromonas, Prevotella, Bacteroides/ Spirochetes: Treponema, & Borrelia o Most common bacteria  -hemolytic strep (Strep viridans) - Streptococcus mutans is most often implicated in plaque formation & leading contributor to cavities & tooth decay.  GIT o Stomach: acidic (pH= 1.5)→ No flora EXCEPT GN Helicobacter pylori (peptic ulcers o Small Intestines: - duodenum Bile is preventive - jejunum & ileum Staph, Lactobacillus, Streptobacillus, Veillonella & C. perfringens. 4  o Colon: largest number & variety of MOs in the human body; - Obligate anaerobes:  GPC: Peptostreptococcus  GNC: Veillonella  GPB: Actinomyces, Clostridium, Bifidobacterium, & Eubacterium  GNB: Fusobacterium, Bacteroides - Facultative anaerobes:  GNB: Escherichia, Klebsiella, Enterobacter, Proteus, Pseudomonas  GPC: Staph & Strep, Enterococcus  GPB: Lactobacilli - many fungi, protozoa & viruses o Opportunistic on changing habitat + Indicators of water fecal contamination  Urogenital Tract o Healthy kidney, ureters, & urinary bladder: sterile o Acidic urine mechanically flush distal urethra & its external meatus: - GPC: Staph, Strep, enterococci - GNC: nonpathogenic Neisseria spp - GPB: Diphtheroids - enteric GNB, anaerobesm, mycoplasma, mycobacteria, yeasts & viruses. o Anatomical or physiological abnormalities→ persistent recurrent UTIs. o Most frequent causes of urethritis: Chlamydia trachomatis, gonococcus, & mycoplasmas. o ♂/♀ reproductive systems: usually sterile EXCEPT vagina - Staph, -hemolytic Strep, Diphtheroids, Actinomyces, Klebsiella, Proteus, & Pseudomonas, Bacteroides, Mycoplasma, yeasts - During puberty & after menopause alkaline - During Childbearing years acidic due to the presence of Lactobacilli. o oral contraceptives→ pH→ Lactobacilli → Susceptibility to Infections: 1. Gardnerella vaginalis, Mobiluncus, Bacteroides, & anaerobic cocci→ Bacterial Vaginosis 2.  C albicans→ yeast vaginitis.  Healthy carriers: carries the microbe but don’t have any symptoms (asymptomatic) o Normal Flora  Nasal/ skin: Staph aureus  Nasopharyngeal: Diphtheria, pertussis, Neisseria meningitides, & pneumonia  Hands: Klebsiella, Pseudomonas, Staphylococcus o Infectious disease (Incubatory, Convalescent & Chronic periods)  EBV, HBV, HIV, Flu, Covid-19, Poliomyelitis  TB & Salmonella typhi (Typhoid Mary) shedding in urine/feces  3C: Cholera, Chlamydia, C. difficile 5  Probiotics (Bio-therapeutic MOs) 1. Oral ingested  harmless MOs - Bacteria as Lactobacillus cultures in yogurt & Yeast as Saccharomyces - reestablish & stabilize intestinal microbial balance by replacing potentially pathogenic MOs.  Prebiotics: non-digestible food ingredients that stimulate growth & activity of intestinal resident bacteria to improve health. 2. Nasal inhaled spray  For treatment of Otitis media → complete or significant recovery.  For prevention of meningitis → ↓ incidence of potentially pathogenic N.meningitidis 3. FMT (Fecal Microbiota Transplantation)  Transfer of intestinal bacteria (FDA approved)  Safe  Stool from healthy donor +saline→ colon of recipient via colonoscopy (most frequently  swallow (24-34 capsules at once; 1 or 2 times)  As a treatment for Recurrent C difficile (≈ twice as effective as Abx) & Ulcerative Colitis  For Prevention of Listeriosis & cholerae (Lactococcus lactis) Biofilms  Definition: complex microbial community embedded in tenacious abundant matrix of hydrated extracellular polymeric substance (EPS), primarily composed of bacterial secreted polysaccharides, proteins, NAs & lipids.  Bacteria grow in tiny clusters (Microcolonies) separated by network of water channels supplying dissolved nutrients & removing waste products.  Co-operative organization: o some specialize in production of surfactants, structural components, & enzymes for matrix production, group motility, & nutrient degradation. o Some feed on metabolic waste of another.  inside, typically divide at very slow rate ( essential nutrients & oxygen)→ Resistant to antibiotics targeting rapidly-dividing cells (Penicillin).  Penicillinase production by some protects others   risk groups: are found in hospital instruments, prosthetics, surgical wounds, burns, bones or extended hospital stays.  MOs can easily detach from biofilm→ tissues & body fluids disease Pathogens of soil  Clostridium spp:  C tetani→ tetanus,  C botulinum → botulism  other C spp→ gas gangrene  Bacillus anthracis→ anthrax.  Various yeasts (Cryptococcus neoformans), & fungal spores 6 Synergistic Infections (Synergism):  Definition: ≥ 2 different MOs produce disease which neither could cause the disease alone→ Synergistic or polymicrobial infections.  Examples:  acute necrotizing ulcerative gingivitis (ANUG) caused by oral flora: spirochetes (Borrelia vincentii) + anaerobes (Fusobacterium & Prevotella & Actinomyces) - oral mucus membranes Trench mouth or Vincent’s stomatitis - pharynx & palatine tonsils Vincent's angina/ ulcero-membranous pharyngitis & tonsillitis  Ludwig’s angina caused by oral flora: Staph (aureus & CONS), Strep (SVG), & anaerobes (Peptostrep, Prevotella, Porphyromonas, Fusobacterium).  Bacterial vaginosis caused by vaginal flora: Gardnerella vaginalis, Mobiluncus spp, Bacteroides & anaerobic cocci. Infectious diseases of farm animals:  Zoonoses: any disease or infection that is naturally transmissible from vertebrate animals to humans category disease Prion disease Scrapie, bovine spongiform encephalopathy “mad cow disease” Viral disease Influenza, rabies, swine pox, foot-and-mouth disease, warts, equine encephalomyelitis (sleeping sickness), vesicular stomatitis Bacterial disease Anthrax, botulism, brucellosis, actinomycosis, anaplasmosis, leptospirosis, campylobacteriosis, listeriosis, pasteurellosis, salmonellosis, tuberculosis, vibriosis Fungal disease ringworms Protozoal disease Babeseiosis, cryptosporidiosis, coccidiosis Bioremediation  Use of genetically engineered bacteria to decompose & clean various types of wastes including industrial wastes (petroleum oil spills)  Use of naturally-occurring bacteria (methanotrophs) to remove highly toxic solvents from soil. 7